Henry Rzepa's Blog

Bonds are a good example of something all chemists think they can recognise when they see them. But they are also remarkably dependent on context. We are running a molecular modelling course at the moment, and I found myself explaining to someone how very context-sensitive they can be. I thought it might be useful to collect my thoughts here.

1. The most primitive bond is the connection type. This is used in chemical informatics to define a connection table for a molecule, which is used by all the major chemical databases to index and hence search for molecules. It is also used by the InChI identifier to create the InChI key, and of course SMILES strings. The connection bond has no other properties (such as its bond order etc), but it is assumed to be covalent rather than ionic.
2. The next is the display bond. This is used by chemical visualisation programs; it is normally created by the code based on very simple rules, such as how far apart the two (or more) atoms are. Such bonds are normally drawn with straight lines, of which there can be up to five (or six at a pinch) nowadays. There is however only a fuzzy convention for how non-integer bond orders are represented. A dashed line can be added (and it might be the only line for weaker types such as hydrogen bonds), but its clear this display convention is suffering at this stage.
   • Perhaps to keep the synthetic chemists happy, I should add two flavours to this category, the stereochemical display bond, which attempts to add a 3D context but in truth does this less than perfectly and the retrosynthetic bond. I will not dwell.
3. Then there is what I call the mechanical bond. This is used in molecular mechanics force fields. It is a declared bond, i.e. you declare where you want the bond to be, and once that is done, it remains there (it is thus never broken). Each declaration is associated with (quadratic) force constants, which taken as a whole define the force field.
4. Next comes the quantum chemical bond. This is defined by a wavefunction, which in turn tells us about the electron density. This, to be frank, can be a can of worms. There must be dozens of ways of interpreting the electron density in terms of a bond type. I have used just one of these on this blog, the ELF procedure, which gives an estimate of how many electrons are involved in any bond (and these are always non-integers). Books could be written about this topic, but I will mention just three varieties which indicate how confusing quantum bonds can become. These are the homo(aromatic) bond, which itself comes in two varieties, bond and no-bond types (DOI: 10.1021/jp026521l), bent bonds and transition state bonds. Phew!
5. The quantum topological bond emerges from  Bader’s QTAIM procedure, which provides a formal topological framework for defining what a bond is. As I noted in earlier posts, it is controversial, since it does not always reflect what chemists might regard as a useful definition that helps them do chemistry.
6. Finally (?), I could add Rydberg bonds, which are mysterious formations on excited state surfaces, and which can be extraordinarily long (> 500Å), thus defying application of simple distance rules as noted in type 2 above.

Tags: chemical databases, chemical informatics, chemical visualisation programs, quantum chemical bond, Tutorial material

This entry was posted on Thursday, October 13th, 2011 at 11:22 am and is filed under Chemical IT, General. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.